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Benchmarking Data

HapMap

HapMap Data Table

Cell Line Data
Benchmarking Tissue Data

HapMap Cell Line Data

For the SMaHT benchmarking study, six cell lines profiled in the International HapMap project (hence the “HapMap” cell lines) were mixed at Coriell, and the cell mixture samples were distributed to GCCs and TTDs for analyses.

Information about the six HapMap cell lines and mixture ratios are the following:

  • 0.5%: HG00438 (Female; Chinese Han in the South)
  • 2%: HG002 (Male; Ashkenazim Jewish)
  • 2%: HG02257 (Female; African Caribbean in Barbados)
  • 2%: HG02486 (Male; African Caribbean in Barbados)
  • 10%: HG02622 (Female; Gambian in Western Division, Mandinka)
  • 83.5%: HG005 (Male; Chinese)

For the MEI Detection Challenge, DAC used the bulk WGS data from BCM-GCC to downsample the HapMap mixture data to 50X, 100X, 200X, and 300X for Illumina (originally ~400X); and to 30X, 60X, and 90X for PacBio and ONT (originally ~100X each).